Hello I have trnascripts.gtf as a cufflinks output. I also downloaded the miRNA annotation in gff3 for mus musculus( ftp://mirbase.org/pub/mirbase/CURRENT/genomes/mmu.gff3)
Is it possible to get the intersection of these two files, meaning extract miRNA information from the assembled transcript?
Thanks for all your input in advance
1 answer
Assuming your data is from regular RNAseq, you can obtain some level of information. You can obtain some expression level for the pre-miRNA forms or poly-cistronic miRNAs, specially if the miRNA is intronic, but this level will be at the level of the associated gene. In my opinion, I will not trust such quantifications, for miRNA is better to quantify only small RNAs to see the expression of the active form.
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